One other thing Greg mentioned that I completely forgot about was the gas cap vent.
Open it up, leave it open. Go for a ride. Intentionally replicate the scenario where the bike shuts off, and see if you still have the shutting off issue when you decelerate. Sometimes the gas caps like to hold a vacuum.
SIDE NOTE:
faq.ninja250.org is an awesome place for information. ninjette.org is still a better site for talking to people about the instructions though
